This is a thought-experiment as I have no idea as to how I'd actually do this (and FS2 isn't installed so I can't test right now - new computer + discs at a friend who is away's house)
The simplest way to make the shield hit's small would be to treat the hits on capships as though they were decals. Since your hitting a fairly flat surface (of the shield) to begin with, what we do is simply draw a new polygon onto the shield exactly where we hit it, sized to the shield hit animation size. Apply a little more of the logic decal's use, and you can make this draw multiple poly's if it hits and intersection and then adjust the UV coords so the animation play's as one.
Problem solved. Anyone who wants to try and code this, I suggest looking up how you do it on the net - there's plenty of info - starting here is recommended
www.gamedev.net